4OJM | pdb_00004ojm

Crystal structure of a C-terminally truncated CYT-18 protein including N-terminal residues

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y42

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.88	α = 90
b = 73.21	β = 111.35
c = 56.79	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-D	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.95	58.58	94.87			25832	25832

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1Y42	1.95	58.58	25832	1936	94.87	0.17081	0.16727	0.18	0.21125	0.22	RANDOM	32.789

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.2		0.43	-1.53		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.08
r_dihedral_angle_4_deg	13.673
r_dihedral_angle_3_deg	12.532
r_long_range_B_refined	7.094
r_long_range_B_other	7.029
r_dihedral_angle_1_deg	5.455
r_scangle_other	4.263
r_mcangle_other	3.545
r_mcangle_it	3.54
r_scbond_it	2.695
r_scbond_other	2.694
r_mcbond_it	2.33
r_mcbond_other	2.321
r_angle_refined_deg	1.127
r_angle_other_deg	0.736
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3071
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement